Haze is an annual problem during the monsoon season from May to September as winds blow the smoke across the Malacca Strait to Malaysia.
Environment Department Director-General Halimah Hassan said they had detected 46 hotspots in Sumatra via satellite.
The Air Pollutant Index (API) showed unhealthy levels of between 101 and 129 in six areas on Sunday morning, including two places in Malacca state along with Port Dickson and the country's largest port, Port Klang.
In the capital Kuala Lumpur the skies were hazy with air pollution readings at 92, just below the unhealthy threshold.
A level of 101-200 is considered unhealthy, while 51-100 is moderate.
Halimah, in a statement late Saturday, attributed the haze to the westerly monsoon season during which winds blow the smoke towards Malaysia.
Haze, mostly caused by fires in Indonesia, builds up during the dry season, affecting tourism and contributing to health problems across the region.
Indonesia's government has outlawed land-clearing by fire but weak law enforcement means the ban is largely ignored.
The haze hit its worst level in 1997-1998, costing the Southeast Asian region an estimated $9 billion by disrupting air travel and other business activities. - AFP